Get Bioentity from Organism
Created: 2009-09-08 15:12:57
Last updated: 2009-09-14 14:16:40
GeNS workflow that lists the identifiers corresponding to a given species and data type. For instance, list all OMIM associated with the human species.
Disclaimer: This workflow is just a simple example designed for academic purposes.
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Workflow Components
Authors (1)
Titles (1)
Descriptions (1)
| Sample workflow to get all GeNS bioentities related to a given organism and data type. |
Dependencies (0)
Inputs (2)
| Name |
Description |
| Organism |
The desired Organism
|
| DataType |
The desired Data Type
|
Processors (19)
| Name |
Type |
Description |
| SearchBioEntity |
wsdl |
Wsdlhttp://bioinformatics.ua.pt/GeNS/WS/Service.asmx?wsdlWsdl OperationSearchBioEntity |
| SearchBioEntityIn |
xmlsplitter |
|
| SearchBioEntityOut |
xmlsplitter |
|
| ListDataTypes |
wsdl |
Wsdlhttp://bioinformatics.ua.pt/GeNS/WS/Service.asmx?wsdlWsdl OperationListDataTypes |
| ListDataTypesIn |
xmlsplitter |
|
| ListDataTypesOut |
xmlsplitter |
|
| SelectTaxId |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
| TaxIdQuery |
stringconstant |
Value//*[local-name()="TaxonomicId"] |
| SearchOrganism |
wsdl |
Wsdlhttp://bioinformatics.ua.pt/GeNS/WS/Service.asmx?wsdlWsdl OperationSearchOrganism |
| SearchOrganismIn |
xmlsplitter |
|
| SearchOrganismOut |
xmlsplitter |
|
| SelectDataType |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
| DataTypeQuery |
stringconstant |
Value//*[local-name()="DataTypeId"] |
| ConcatTaxIdComma |
localworker |
Scriptoutput = string1 + string2; |
| Comma |
stringconstant |
Value, |
| ConcatTaxIdCommaDataType |
localworker |
Scriptoutput = string1 + string2; |
| SelectAlias |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
| AliasQuery |
stringconstant |
Value//*[local-name()="Alias"] |
| AliasList2String |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
Datalinks (22)
| Source |
Sink |
| SearchBioEntityIn:output |
SearchBioEntity:parameters |
| ConcatTaxIdCommaDataType:output |
SearchBioEntityIn:data |
| SearchBioEntity:parameters |
SearchBioEntityOut:input |
| ListDataTypesIn:output |
ListDataTypes:parameters |
| DataType |
ListDataTypesIn:data |
| ListDataTypes:parameters |
ListDataTypesOut:input |
| TaxIdQuery:value |
SelectTaxId:xpath |
| SearchOrganismOut:SearchOrganismResult |
SelectTaxId:xml-text |
| SearchOrganismIn:output |
SearchOrganism:parameters |
| Organism |
SearchOrganismIn:data |
| SearchOrganism:parameters |
SearchOrganismOut:input |
| DataTypeQuery:value |
SelectDataType:xpath |
| ListDataTypesOut:ListDataTypesResult |
SelectDataType:xml-text |
| SelectTaxId:nodelist |
ConcatTaxIdComma:string1 |
| Comma:value |
ConcatTaxIdComma:string2 |
| ConcatTaxIdComma:output |
ConcatTaxIdCommaDataType:string1 |
| SelectDataType:nodelist |
ConcatTaxIdCommaDataType:string2 |
| AliasQuery:value |
SelectAlias:xpath |
| SearchBioEntityOut:SearchBioEntityResult |
SelectAlias:xml-text |
| Comma:value |
AliasList2String:seperator |
| SelectAlias:nodelist |
AliasList2String:stringlist |
| AliasList2String:concatenated |
Final |
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Sample Entity Converter
(1)
Disclaimer: This workflow is just a simple example designed for academic purposes.
Created: 2009-09-08
| Last updated: 2009-09-14
Credits:
Pedro Lopes
Search GeNS BioEntity
(1)
This workflow returns a list of know associations between an organism and a data type. All identifiers correspond to GeNS database identifiers.
Disclaimer: This workflow is just a simple example designed for academic purposes.
Created: 2009-09-15
| Last updated: 2009-09-15
Credits:
Pedro Lopes
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